We see that many words in the VM comply with a comparatively simple and straightforward grammar, but we also see that lots of words break with those rules — hence, the underlying rules are either more complex than we think, or not all words must obey them.
To paraphrase this in terms of the Stroke theory, it means that a character set of 26 capital and 26 minor letters plus 10 digits apparently was not enough to transcribe the VM plaintext, otherwise we’d only see 62 different “syllables” making up the VM.
Now, idly browsing across the web I came across a German astronomical manuscript from around 1500. If you take a look at f28r —
(click the image to get the full resolution), you’ll notice that while the top half of the page consists almost entirely of the latin alphabet, the bottom section is riddled with astrological symbols.
If such was the case with the VM itself, these “special characters” would require special enciphering: Some graphical elements in those symbols aren’t present in the latin character set, which would give rise to the use of rare ciphertext letters, plus their combinations would be different from the grammar of the body of the text. Hence, we’d have occurences of unusual letters and breach of the grammar rules.
Under this assumption, the hypothesis would be that the VM word “grammar” is not so much a grammar per se, but rather an artifact of the existance of only a limited set of syllables to begin with.